1. Field of the Invention
The present invention relates to screening methods for amphiphilic peptides binding specifically to hairpin RNA, more precisely to screening methods for amphiphilic peptides having target hairpin RNA specificity and powerful binding force as well by using peptide libraries in which the hydrophilic face and hydrophobic face of the amphiphilic peptide are changed.
2. Description of the Related Art
RNA hairpins share similarities in morphology and play a very important role in gene expression, etc, from prokaryotes to eukaryotes. Therefore, such RNA molecules can be targets for drugs. In particular, hairpin RNAs have deep grooves similar to DNA, to which low molecular substances can be conjugated. There are many RNA binding low-molecular compounds but their binding force and specificity have been always in question.
Peptides are believed to be a promising alternative for such low-molecular substances, which is supported by the identification of Rev peptide having strong binding force and specificity to natural hairpin RNA. The present inventors also confirmed previously that an amphiphilic peptide having alpha-helix structure could bind specifically to hairpin RNA. There are some other natural peptides specific to hairpin RNA; however, a method to produce ligands specific to hairpin RNA by using such alpha-helical peptides has not been established. Encouraged by the activity of natural peptides, amphiphilic peptides composed of leucine and lysine have been prepared.
It is difficult to distinguish target hairpin RNA molecules because of their high similarity. In addition, hairpin RNA has a more promiscuous structure than other RNAs. Accordingly, it is very difficult to prepare a ligand specific to non-selective hairpin molecules without preparatory study. Recent techniques cannot even distinguish hairpin molecules having promiscuous structure from that with simple structure.
Amphiphilic peptides generally conjugate well to hairpins. When slightly modified but non-narrowed peptides were conjugated to various hairpins, the binding force was not much different from that to hairpin of wide-open structures. But, some specific hairpins are presumed to be useful to separate non-narrowed peptides. So it is believed alanine-scanned peptide libraries might be a help to judge the complexity of the target hairpin.
The present inventors synthesized an amphiphilic peptide binding to hairpin RNA whose hydrophilic face and hydrophobic face are modified and further completed this invention by establishing a method for screening the amphiphilic peptide which has better specificity to hairpin RNA and stronger binding force as well than the natural amphiphilic peptide.